Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1650 to 1699 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
825	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [source:swissprot;acc:o43516]	Divided	206.214	197.614	1.04352	
826	60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [source:swissprot;acc:q92993]	Divided	223.186	213.912	1.04335	
826	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [source:swissprot;acc:p52435]	Subtracted	230.811	239.785	8.974	
827	jm1 protein. [source:refseq;acc:nm_014008]	Subtracted	219.762	210.806	8.956	
827	loh1cr12. [source:refseq;acc:nm_058169]	Divided	230.087	220.579	1.0431	
828	ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm_006395]	Subtracted	135.087	144.041	8.954	
828	unr protein. [source:swissprot;acc:o75534]	Divided	230.087	220.579	1.0431	
829	dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [source:swissprot;acc:p28715]	Subtracted	252.873	261.821	8.948	
829	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236]	Divided	135.844	130.259	1.04288	
830	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [source:refseq;acc:nm_004562]	Divided	231.734	222.222	1.0428	
830	wd-repeat protein 3. [source:swissprot;acc:q9unx4]	Subtracted	243.896	234.96	8.936	
831	60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	Subtracted	229.171	238.048	8.877	
831	hepatoma-derived growth factor-related protein 2. [source:refseq;acc:nm_032631]	Divided	231.734	222.222	1.0428	
832	cgi-142; hepatoma-derived growth factor 2. [source:refseq;acc:nm_016073]	Divided	231.734	222.222	1.0428	
832	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [source:refseq;acc:nm_032243]	Subtracted	229.171	238.048	8.877	
833	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [source:refseq;acc:nm_033222]	Divided	231.734	222.222	1.0428	
833	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [source:swissprot;acc:p10599]	Subtracted	229.171	238.048	8.877	
834	60s ribosomal protein l8. [source:swissprot;acc:p25120]	Divided	231.734	222.222	1.0428	
834	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [source:refseq;acc:nm_032959]	Subtracted	230.768	239.632	8.864	
835	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [source:swissprot;acc:p51858]	Divided	231.734	222.222	1.0428	
835	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [source:swissprot;acc:q07244]	Subtracted	224.413	233.272	8.859	
836	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [source:refseq;acc:nm_138574]	Divided	231.734	222.222	1.0428	
836	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [source:swissprot;acc:o43172]	Subtracted	224.413	233.272	8.859	
837	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [source:swissprot;acc:p26196]	Divided	231.734	222.222	1.0428	
837	structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [source:swissprot;acc:q08945]	Subtracted	237.62	228.762	8.858	
838	chromatin-specific transcription elongation factor large subunit. [source:refseq;acc:nm_007192]	Subtracted	237.62	228.762	8.858	
838	rw1 protein (fragment). [source:swissprot;acc:q92545]	Divided	231.734	222.222	1.0428	
839	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [source:refseq;acc:nm_145325]	Subtracted	230.764	239.62	8.856	
839	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [source:refseq;acc:nm_002975]	Divided	177.776	170.499	1.04268	
840	deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [source:swissprot;acc:o75398]	Subtracted	236.741	245.547	8.806	
840	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [source:swissprot;acc:q15388]	Divided	198.781	190.66	1.04259	
841	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [source:swissprot;acc:p40855]	Divided	198.781	190.66	1.04259	
841	rio kinase 1 isoform 1; ad034 protein. [source:refseq;acc:nm_031480]	Subtracted	236.741	245.547	8.806	
842	jm1 protein. [source:refseq;acc:nm_014008]	Divided	219.762	210.806	1.04248	
842	map/microtubule affinity-regulating kinase 1. [source:refseq;acc:nm_018650]	Subtracted	236.741	245.547	8.806	
843	map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [source:refseq;acc:nm_004954]	Subtracted	236.741	245.547	8.806	
843	trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [source:swissprot;acc:p22102]	Divided	218.521	227.796	1.04244	
844	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [source:swissprot;acc:o75596]	Divided	178.033	170.82	1.04223	
844	meiotic recombination protein spo11. [source:swissprot;acc:q9y5k1]	Subtracted	236.741	245.547	8.806	
845	hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [source:swissprot;acc:q9nyq3]	Subtracted	232.512	241.288	8.776	
845	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [source:swissprot;acc:o15116]	Divided	228.599	219.399	1.04193	
846	methyltransferase like 2. [source:refseq;acc:nm_018396]	Divided	147.211	153.371	1.04184	
846	parafibromin. [source:refseq;acc:nm_024529]	Subtracted	239.704	230.991	8.713	
847	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763]	Divided	147.211	153.371	1.04184	
847	l-myc-1 proto-oncogene protein. [source:swissprot;acc:p12524]	Subtracted	227.604	219.001	8.603	
848	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	Divided	147.211	153.371	1.04184	
848	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [source:swissprot;acc:o43516]	Subtracted	206.214	197.614	8.6	
849	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [source:swissprot;acc:q92824]	Divided	147.211	153.371	1.04184	
849	transcription factor iib. [source:refseq;acc:nm_013242]	Subtracted	206.068	197.471	8.597	
850	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [source:refseq;acc:nm_006693]	Divided	107.842	112.329	1.04161	

Legend:
- Rank is the rank after comparing the two networks
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/